Contacts of the strand formed by residues 61 - 66 (chain J) in PDB entry 4NL3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 61 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G PHE* 3.5 23.5 - - + +
59G HIS* 2.7 33.6 + - - -
25J VAL* 3.9 17.3 - - + -
26J PHE 4.0 2.9 - - - -
27J LEU* 4.2 5.6 - - + -
28J THR* 4.0 1.6 + - - -
45J VAL* 4.0 29.6 - - + -
47J LEU* 5.9 1.1 - - + -
56J VAL* 3.6 25.1 - - + -
57J PHE 3.5 10.3 - - - +
58J LYS* 3.0 16.7 + - + +
60J ALA* 1.3 78.4 - - - +
62J SER* 1.3 62.1 + - - +
63J THR 4.1 5.8 - - - +
64J PHE* 3.9 22.2 - - + -
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Residues in contact with SER 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LEU* 3.5 27.7 - - - +
29G ASN* 4.2 6.5 + - - -
56G VAL* 3.5 3.1 - - - +
57G PHE* 2.9 29.8 + - - +
60G ALA* 3.5 20.5 - - - +
26J PHE* 2.8 20.7 + - - +
27J LEU 4.0 15.5 - - - -
28J THR* 4.1 5.4 - - - -
60J ALA 3.8 0.6 + - - -
61J ILE* 1.3 73.7 - - - +
63J THR* 1.3 64.8 + - - +
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Residues in contact with THR 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 3.9 14.1 - - + -
33G LEU* 4.3 7.4 - - + -
54G GLN* 4.7 10.3 + - - -
55G LEU 3.1 8.3 - - - -
56G VAL* 3.7 26.2 - - + -
57G PHE* 5.0 0.2 - - - -
24J THR 3.8 0.2 - - - +
25J VAL* 3.8 7.1 - - - +
26J PHE* 3.3 48.5 + - + +
61J ILE* 4.1 0.8 - - - +
62J SER* 1.3 95.2 - - - +
64J PHE* 1.3 68.1 + - - +
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Residues in contact with PHE 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G GLN* 3.8 2.5 - - - -
55G LEU* 2.5 49.5 + - + +
57G PHE* 3.6 35.0 - + - -
12J TYR* 5.0 1.3 + - + -
13J LEU* 3.7 31.4 - - + -
16J LEU* 4.3 20.0 - - + -
23J ALA* 4.6 7.2 - - + -
24J THR 4.1 0.4 - - - -
25J VAL* 3.6 28.7 - - + -
37J VAL* 4.5 13.9 - - + -
45J VAL* 4.4 12.8 - - + -
47J LEU* 5.0 2.5 - - + -
61J ILE* 3.9 25.8 - - + -
63J THR* 1.3 72.3 - - - +
65J SER* 1.3 59.5 + - - +
66J PRO* 3.4 8.3 - - - +
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Residues in contact with SER 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LYS* 2.8 26.7 + - - -
54G GLN* 3.1 22.9 + - - +
23J ALA* 3.2 3.1 - - - +
24J THR* 2.6 56.7 + - - +
26J PHE* 4.5 12.3 - - - -
34J ARG* 4.9 1.0 + - - -
63J THR* 5.2 0.2 - - - -
64J PHE* 1.3 72.5 - - - +
66J PRO* 1.3 61.9 - - - +
67J GLN 4.1 0.2 + - - -
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Residues in contact with PRO 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LYS* 2.8 27.2 + - - +
53G GLN* 3.3 25.8 - - + +
12J TYR* 3.2 25.6 - - + +
16J LEU* 4.0 22.7 - - + -
21J ILE* 4.2 1.6 - - + -
22J LEU 3.7 5.6 - - - +
23J ALA* 3.9 3.8 - - + -
34J ARG* 6.0 0.2 - - - -
64J PHE 3.4 7.9 - - - +
65J SER* 1.3 85.8 - - - +
67J GLN* 1.3 63.2 + - - +
68J LYS 3.3 22.6 - - - +
69J ASN* 4.8 1.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il